The primary goal of this application is to identify genes and other genomic features that underlie the action of alcohol. While we have made considerable progress toward this objective through the use mouse quantitative trait loci (QTL) mapping, gene expression profiling and comparative DNA sequencing, these studies were limited and complicated by two newly discovered factors related to the analysis of complex traits 1) mammalian genomic variation, including copy number variation (CNV), is much more prevalent than previously expected , and 2) mouse genome sequence contains many gaps and complex, duplication-rich regions that are likely to be misassembled. We plan to apply two recently developed genomic strategies that circumvent many of these limitations. The first strategy will be to carry out very high density array-based comparative genomic hybridization (aCGH) of several mouse strains (ILS, ISS, LXS RIs and HS4) known to differ in alcohol-related phenotypes, and identify CNVs that are contributing to differences in alcohol action between these strains. CNVs will be independently confirmed, CNV boundaries fine-mapped using custom aCGH arrays, and genes within the CNV identified and characterized. To our knowledge this study will be the first genome-wide investigation of the role of CNVs in alcohol action. The second strategy will be to obtain and compare the complete DNA sequences of four QTL regions (Lores1, 2, 4, and 5) between strains that have been selected for differential sensitivity to alcohol (ILS and ISS). This will be carried out by array-capture of QTL- specific DNAs from each strain, followed by ultra-high throughput DNA sequencing of the complete QTL interval using next generation DNA sequencing technology. This study will identify all DNA sequence variations within each Lore QTL and, as such, will represent the most complete assessment of genomic variation with these alcohol-related QTLs.